Page contents:

On this page, you can find R/Bioconductor libraries for Unix/Linux
and Windows:
1. Bioconductor support libraries for the human and mouse NuGO
arrays.
2. Bioconductor annotation libraries for the Affymetrix Gene Titan
system that are not provided by the Bioconductor project.
3. Bioconductor CDF libraries for the Affymetrix gene ST arrays and
Gene Titan System that are not (or not proper) provided by the
Bioconductor project.
4. Bioconductor libraries for the MBNI
Custom Chip Definition Files (CDFs) for the human and mouse NuGO
arrays (cdf, probe, and Entrez gene annotation).
5. For the current MBNI
Custom Chip Definition Files (CDFs) release: Bioconductor libraries
for human, mouse, and rat species that we support (Entrez gene; also
probe and cdf)*.
6. For the previous MBNI
Custom Chip Definition Files (CDFs) release: Bioconductor libraries
for human, mouse, and rat species that we support (Entrez gene; also
probe and cdf)*.

*: For
convenience, we mirror the probe and CDF files as provided by MBNI.
The version 14.1.0. annotation libraries, as hosted by MBNI, are
complient with Bioconductor. These packages are mirrorred here (and
not created by ourselves). In case MBNI provides no annotation
libraries, these are created by ourselves. We provide only the
Entrezg libraries, and tairg for Arabidopsis.

REMARK:
we decided to use the ENTREZ Custom CDF-files for the following
reasons:

Most up-to-date.

Corresponds to genes (not transcripts).

Accepted input for follow-up analyses.

Off course, you are free to use one of the other formats, e.g.
ENSEMBL, but we do not provide Bioconductor annotation libraries for
those custom CDFs.

Custom CDFs:Please do this if you receive an error message on missing
libraries (only the lacking libraries need to be installed):
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("org.At.tair.db", "org.Hs.eg.db",
"org.Mm.eg.db", "org.Rn.eg.db"))

Current Custom CDf is version 14.1.0 (March 11 2011). Previous
Custom CDF is version 13.0.0 (July 6 2010).
If new Custom CDF libraries are released, the versions will shift up
(and the current "previous" repository will be dropped).
Please check the tables below to see whether your chip is supported!
Simply use the proper library names in the commands as shown in the
examples above.

Manual Installation

Installation instructions

For Windows: download the appropriate .zip-files from the tables
below. In RGui, go to Packages => Install package(s) from local
zip-files... Browse to the location where you downloaded your
.zip-files and select the files you want to install. Done!

For Unix/Linux: download the appropriate .tar.gz files from the
tables below. cd to the directory where you downloaded your .tar.gz
files and execute the following command (multiple times for multiple
.tar.gz files): R CMD INSTALL <your downloaded .tar.gz file>.

Download tables

1. Human and mouse NuGO array support files as provided on the
Bioconductor web site (7 November 2011).
Here, also the CDF and PROBE libraries are
available for download. To obtain full microarray support, you need
to download and install all three libraries for each chip!

2. Human and mouse NuGO array support files (VERSION
14.1.0 (cdf, probe) & version 14.1.1 (.db); MBNI
Custom CDF; updated 7 November 2011).
To obtain full microarray support, you need to download and install
all three libraries for each chip!

3. Annotation libraries for the
Affymetrix GeneTitan plates (based on the
AFFYMATRIX probe annotations). Updated 7 November
2011).
The CDF and PROBE libraries are available on http://www.bioconductor.org
or via the biocLite()
command.
To obtain full microarray support, you need to
download and install all three libraries (cdf. probe, and .db) for
each chip!

4. Affymetrix derived CDF
libraries for the gene ST arrays and the GeneTitan plates (Updated
7 November 2011).
These CDF-files are created utilizing oligo and
the PdInfo2Cdf.R
script.
More information on the procedure is available
here
and here.

5. Annotation libraries for the MBNI
Custom CDF annotation files (mirrored from MBNI; VERSION
14.1.0 (cdf, probe) & version 14.1.1 (.db); updated 7
November 2011). Here,
also the CDF and PROBE libraries are available for download. To
obtain full microarray support, you need to download and install all
three libraries for each chip!

6. Human and mouse NuGO array support files (VERSION
13.0.0 (cdf, probe) & version 13.0.3 (.db); MBNI
Custom CDF; updated 7 November 2011).
Here, also the CDF and PROBE libraries are
available for download. To obtain full microarray support, you need
to download and install all three libraries for each chip!

7. Annotation libraries for the MBNI
Custom CDF annotation files (VERSION 13.0.0 (cdf.probe) & version 13.0.3 (.db);
updated 7 November 2011). Here,
also the CDF and PROBE libraries are available for download. To
obtain full microarray support, you need to download and install all
three libraries for each chip!